We generate source code into a "src/main/generated" directory. IntelliJ picks it up like any other source code with proper Gradle configuration and we ignore it with .gitignore.

Only downside we've found is it can be a pain with searching for references in Github and you have to remember to generate the code, but for the most part it is seamless.

I guess how you manage it depends on your IDE, if you can configure it to work nicely, and how much the generated source changes/needs to be read.